Re: [VCFtools-spec] VCF 4.2 GLE field

[Joachim B. <ki...@co...>]

Hi Petr,

  I got an off-the-list reply from Erik Garrison earlier and he thinks it is not widely used either.

  For now, if I encounter GLE in a file, I will simply interpret it as a string value — unless it breaks the formatting completely.

  I am looking forward to the 4.3 spec by the way! Great stuff!

Thanks,

Kim

CODAMONO, Toronto, Ontario, Canada.

On June 11, 2015 at 11:03:31 AM, Petr Danecek (pd...@sa...) wrote:

Hi Joachim,  

I think this was meant verbatim, otherwise the field would be defined as  
Type=Float, not as String.  

This is a bug in the specification which went unnoticed since v4.1,  
apparently no one has been using the field. I did not find any mention  
about GLE other than this  
http://sourceforge.net/p/vcftools/mailman/message/30123755/  

I've open an issue on github for this  
https://github.com/samtools/hts-specs/issues/90  

Perhaps a semicolon could be used a separator instead?  

Cheers,  
Petr  




On Thu, 2015-05-28 at 10:38 -0400, Joachim Baran wrote:  
> Hello,  
>  
>  
> I am working on a bioinformatics tool for bringing genomics data  
> (GFF3, GTF, GVF, VCF formats) into the cloud and storing it in NoSQL  
> databases (MongoDB, RethinkDB, Elasticsearch, etc.).  
>  
>  
> Most of the VCF 4.2 specification is quite clear, but I am having  
> trouble understanding the formatting of the GLE field. The example  
> provided in the specification is  
> "0:-75.22,1:-223.42,0/0:-323.03,1/0:-99.29,1/1:-802.53”.  
>  
>  
> Does the example mean that colons can appear in the GLE field —  
> despite the fact that colons are already used to separate genotype  
> fields? Or, does the example mean that the likelihoods are provided  
> with a GLE field value of  
> “-75.22,-223.42,-323.03,-99.29,-802.53” (comma separated), which  
> correspond to the genotype ordering 0, 1, 0/0, 1/0, 1/1?  
>  
>  
> I would appreciate if someone could clarify this part of the  
> specification. Thank you.  
>  
>  
> Best wishes,  
>  
> Kim  
>  
>  
> CODAMONO, Toronto, Ontario, Canada.  
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